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   &#160;<span id="projectnumber">2.0.0</span>
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   <div id="projectbrief">An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics</div>
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<a href="beagle_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;<span class="preprocessor">#ifndef __beagle__</span></div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define __beagle__</span></div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;<span class="preprocessor">#include &quot;libhmsbeagle/platform.h&quot;</span></div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div>
<div class="line"><a name="l00120"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfce">  120</a></span>&#160;<span class="keyword">enum</span> <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfce">BeagleReturnCodes</a> {</div>
<div class="line"><a name="l00121"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea12aea4769c1be89867846782925b1cbe">  121</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea12aea4769c1be89867846782925b1cbe">BEAGLE_SUCCESS</a>                      =  0,  </div>
<div class="line"><a name="l00122"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea45c3bd53fdd83865d927202d0d582299">  122</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea45c3bd53fdd83865d927202d0d582299">BEAGLE_ERROR_GENERAL</a>                = -1,  </div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaf31bb198b162f0d9ed2e0490a475409d">  123</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaf31bb198b162f0d9ed2e0490a475409d">BEAGLE_ERROR_OUT_OF_MEMORY</a>          = -2,  </div>
<div class="line"><a name="l00124"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea3fd3b3dc476c527884e6db3dc0d13738">  124</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea3fd3b3dc476c527884e6db3dc0d13738">BEAGLE_ERROR_UNIDENTIFIED_EXCEPTION</a> = -3,  </div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaba333086a5777117202ed0f16109157a">  125</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaba333086a5777117202ed0f16109157a">BEAGLE_ERROR_UNINITIALIZED_INSTANCE</a> = -4,  </div>
<div class="line"><a name="l00127"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea1118b576b6d5e1372f757ec246acd203">  127</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea1118b576b6d5e1372f757ec246acd203">BEAGLE_ERROR_OUT_OF_RANGE</a>           = -5,  </div>
<div class="line"><a name="l00129"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaec9b03ad5cd754a99ed84e1755704beb">  129</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaec9b03ad5cd754a99ed84e1755704beb">BEAGLE_ERROR_NO_RESOURCE</a>            = -6,  </div>
<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea74be6f002aba021c7093dfe50b44f1ed">  130</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea74be6f002aba021c7093dfe50b44f1ed">BEAGLE_ERROR_NO_IMPLEMENTATION</a>      = -7,  </div>
<div class="line"><a name="l00131"></a><span class="lineno"><a class="line" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea267dcbe8ced105decc94598ba2be51ba">  131</a></span>&#160;    <a class="code" href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea267dcbe8ced105decc94598ba2be51ba">BEAGLE_ERROR_FLOATING_POINT</a>         = -8   </div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;};</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;</div>
<div class="line"><a name="l00142"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bdde">  142</a></span>&#160;<span class="keyword">enum</span> <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bdde">BeagleFlags</a> {</div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea6efa1e464b74cfcf6e7317d79bf1c085">  143</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea6efa1e464b74cfcf6e7317d79bf1c085">BEAGLE_FLAG_PRECISION_SINGLE</a>    = 1 &lt;&lt; 0,    </div>
<div class="line"><a name="l00144"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea83963bbb1062fd6c060553de8dd6b429">  144</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea83963bbb1062fd6c060553de8dd6b429">BEAGLE_FLAG_PRECISION_DOUBLE</a>    = 1 &lt;&lt; 1,    </div>
<div class="line"><a name="l00146"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac4e28e01f5d95262033f72410ca57c89">  146</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac4e28e01f5d95262033f72410ca57c89">BEAGLE_FLAG_COMPUTATION_SYNCH</a>   = 1 &lt;&lt; 2,    </div>
<div class="line"><a name="l00147"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac2cf9217aa4e7a2e002746528a8ba29b">  147</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac2cf9217aa4e7a2e002746528a8ba29b">BEAGLE_FLAG_COMPUTATION_ASYNCH</a>  = 1 &lt;&lt; 3,    </div>
<div class="line"><a name="l00149"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea96ef202a6ec8fc3754dc3095b30a87fb">  149</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea96ef202a6ec8fc3754dc3095b30a87fb">BEAGLE_FLAG_EIGEN_REAL</a>          = 1 &lt;&lt; 4,    </div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea5a64736d6ca8cd54532e35f597671f16">  150</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea5a64736d6ca8cd54532e35f597671f16">BEAGLE_FLAG_EIGEN_COMPLEX</a>       = 1 &lt;&lt; 5,    </div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea44746eb12a08bd5427ecf7e0508e02e9">  152</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea44746eb12a08bd5427ecf7e0508e02e9">BEAGLE_FLAG_SCALING_MANUAL</a>      = 1 &lt;&lt; 6,    </div>
<div class="line"><a name="l00153"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea78667e7bb79ac6c002d0180d3e27d6b5">  153</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea78667e7bb79ac6c002d0180d3e27d6b5">BEAGLE_FLAG_SCALING_AUTO</a>        = 1 &lt;&lt; 7,    </div>
<div class="line"><a name="l00154"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea11d8bbb56c0d104bf29e877f90f12935">  154</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea11d8bbb56c0d104bf29e877f90f12935">BEAGLE_FLAG_SCALING_ALWAYS</a>      = 1 &lt;&lt; 8,    </div>
<div class="line"><a name="l00155"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea8c750c64eb7c532c40a1b520c7253656">  155</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea8c750c64eb7c532c40a1b520c7253656">BEAGLE_FLAG_SCALING_DYNAMIC</a>     = 1 &lt;&lt; 25,   </div>
<div class="line"><a name="l00157"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea81574eae3cca4fd42b3b34d731555b64">  157</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea81574eae3cca4fd42b3b34d731555b64">BEAGLE_FLAG_SCALERS_RAW</a>         = 1 &lt;&lt; 9,    </div>
<div class="line"><a name="l00158"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea90091808850e51109fcb2f06fc8eb6f3">  158</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea90091808850e51109fcb2f06fc8eb6f3">BEAGLE_FLAG_SCALERS_LOG</a>         = 1 &lt;&lt; 10,   </div>
<div class="line"><a name="l00160"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeadbd1b3e83d25b5fae3a14a724b24cec2">  160</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeadbd1b3e83d25b5fae3a14a724b24cec2">BEAGLE_FLAG_INVEVEC_STANDARD</a>    = 1 &lt;&lt; 20,   </div>
<div class="line"><a name="l00161"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9fc181aac842ebac6d51ccb19cf0e2ca">  161</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9fc181aac842ebac6d51ccb19cf0e2ca">BEAGLE_FLAG_INVEVEC_TRANSPOSED</a>  = 1 &lt;&lt; 21,   </div>
<div class="line"><a name="l00163"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea6f9a787ae342115c27a7437e8b0d9dc6">  163</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea6f9a787ae342115c27a7437e8b0d9dc6">BEAGLE_FLAG_VECTOR_SSE</a>          = 1 &lt;&lt; 11,   </div>
<div class="line"><a name="l00164"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeab55cd0f09a8c91e5d2d51b239515da4a">  164</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeab55cd0f09a8c91e5d2d51b239515da4a">BEAGLE_FLAG_VECTOR_AVX</a>          = 1 &lt;&lt; 24,   </div>
<div class="line"><a name="l00165"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea538654597350cea65553c70189ceb107">  165</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea538654597350cea65553c70189ceb107">BEAGLE_FLAG_VECTOR_NONE</a>         = 1 &lt;&lt; 12,   </div>
<div class="line"><a name="l00167"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac522542d33f45928656aa2dfe478b3ce">  167</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac522542d33f45928656aa2dfe478b3ce">BEAGLE_FLAG_THREADING_OPENMP</a>    = 1 &lt;&lt; 13,   </div>
<div class="line"><a name="l00168"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea444ce15e77f6cfaeb77ee1762925cd77">  168</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea444ce15e77f6cfaeb77ee1762925cd77">BEAGLE_FLAG_THREADING_NONE</a>      = 1 &lt;&lt; 14,   </div>
<div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9aea9b1db1765a059e5f0c994c7ff5b4">  170</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9aea9b1db1765a059e5f0c994c7ff5b4">BEAGLE_FLAG_PROCESSOR_CPU</a>       = 1 &lt;&lt; 15,   </div>
<div class="line"><a name="l00171"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeaf7a580b8584fbdba42c5a1bab2b6ed6c">  171</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeaf7a580b8584fbdba42c5a1bab2b6ed6c">BEAGLE_FLAG_PROCESSOR_GPU</a>       = 1 &lt;&lt; 16,   </div>
<div class="line"><a name="l00172"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9480c27a220b39df8980176376e27bbf">  172</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9480c27a220b39df8980176376e27bbf">BEAGLE_FLAG_PROCESSOR_FPGA</a>      = 1 &lt;&lt; 17,   </div>
<div class="line"><a name="l00173"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea5dcb70fa15d216e8295982953d535ff9">  173</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea5dcb70fa15d216e8295982953d535ff9">BEAGLE_FLAG_PROCESSOR_CELL</a>      = 1 &lt;&lt; 18,   </div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeaad2f12434a5b2882925c836976cf49cc">  174</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeaad2f12434a5b2882925c836976cf49cc">BEAGLE_FLAG_PROCESSOR_PHI</a>       = 1 &lt;&lt; 19,   </div>
<div class="line"><a name="l00175"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea3e2ddc258bd1d83c75bbeff3f57c94d8">  175</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea3e2ddc258bd1d83c75bbeff3f57c94d8">BEAGLE_FLAG_PROCESSOR_OTHER</a>     = 1 &lt;&lt; 26,   </div>
<div class="line"><a name="l00177"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea40c7b4711118fb6fa14e697a698eda87">  177</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea40c7b4711118fb6fa14e697a698eda87">BEAGLE_FLAG_FRAMEWORK_CUDA</a>      = 1 &lt;&lt; 22,   </div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea04dcbc29ff83699be424c21b38e57d06">  178</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea04dcbc29ff83699be424c21b38e57d06">BEAGLE_FLAG_FRAMEWORK_OPENCL</a>    = 1 &lt;&lt; 23,    </div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeacc951e8ceb79f83b91977b2cea646917">  179</a></span>&#160;    <a class="code" href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeacc951e8ceb79f83b91977b2cea646917">BEAGLE_FLAG_FRAMEWORK_CPU</a>       = 1 &lt;&lt; 27   </div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;};</div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;</div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55c">  189</a></span>&#160;<span class="keyword">enum</span> <a class="code" href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55c">BeagleOpCodes</a> {</div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55ca907d2c6aac07be265a496476a55216e5">  190</a></span>&#160;        <a class="code" href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55ca907d2c6aac07be265a496476a55216e5">BEAGLE_OP_COUNT</a>    = 7, </div>
<div class="line"><a name="l00191"></a><span class="lineno"><a class="line" href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55ca2eb262bbe41b1dbeff3e189d8de65b04">  191</a></span>&#160;        <a class="code" href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55ca2eb262bbe41b1dbeff3e189d8de65b04">BEAGLE_OP_NONE</a>     = -1 </div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;};</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;</div>
<div class="line"><a name="l00197"></a><span class="lineno"><a class="line" href="struct_beagle_instance_details.html">  197</a></span>&#160;<span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
<div class="line"><a name="l00198"></a><span class="lineno"><a class="line" href="struct_beagle_instance_details.html#a62da477128f3d7d56b58a97445e5c777">  198</a></span>&#160;    <span class="keywordtype">int</span> <a class="code" href="struct_beagle_instance_details.html#a62da477128f3d7d56b58a97445e5c777">resourceNumber</a>; </div>
<div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="struct_beagle_instance_details.html#a2f95e32bd70ddef33d3676673e1403ff">  199</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="struct_beagle_instance_details.html#a2f95e32bd70ddef33d3676673e1403ff">resourceName</a>; </div>
<div class="line"><a name="l00201"></a><span class="lineno"><a class="line" href="struct_beagle_instance_details.html#a05420095a96892a7da9ca33ec737c4a2">  201</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="struct_beagle_instance_details.html#a05420095a96892a7da9ca33ec737c4a2">implName</a>;     </div>
<div class="line"><a name="l00203"></a><span class="lineno"><a class="line" href="struct_beagle_instance_details.html#a06dd93495752717d4a55a75b3f4452d5">  203</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="struct_beagle_instance_details.html#a06dd93495752717d4a55a75b3f4452d5">implDescription</a>; </div>
<div class="line"><a name="l00204"></a><span class="lineno"><a class="line" href="struct_beagle_instance_details.html#a73d2211c0f0d5b730d7a768155ff0be4">  204</a></span>&#160;    <span class="keywordtype">long</span> <a class="code" href="struct_beagle_instance_details.html#a73d2211c0f0d5b730d7a768155ff0be4">flags</a>;         </div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;} <a class="code" href="struct_beagle_instance_details.html">BeagleInstanceDetails</a>;</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;</div>
<div class="line"><a name="l00211"></a><span class="lineno"><a class="line" href="struct_beagle_resource.html">  211</a></span>&#160;<span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
<div class="line"><a name="l00212"></a><span class="lineno"><a class="line" href="struct_beagle_resource.html#adc4f25e6c9f6b62c0ca00d41fd5e99f7">  212</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="struct_beagle_resource.html#adc4f25e6c9f6b62c0ca00d41fd5e99f7">name</a>;         </div>
<div class="line"><a name="l00213"></a><span class="lineno"><a class="line" href="struct_beagle_resource.html#a529ec0036f2af507febd15940dc0575b">  213</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="struct_beagle_resource.html#a529ec0036f2af507febd15940dc0575b">description</a>;  </div>
<div class="line"><a name="l00214"></a><span class="lineno"><a class="line" href="struct_beagle_resource.html#a114a8e272a9b10d6e2b1629c3ba62fcd">  214</a></span>&#160;    <span class="keywordtype">long</span>  <a class="code" href="struct_beagle_resource.html#a114a8e272a9b10d6e2b1629c3ba62fcd">supportFlags</a>; </div>
<div class="line"><a name="l00215"></a><span class="lineno"><a class="line" href="struct_beagle_resource.html#a84d561923dd65e9bec5a22f2e782a89d">  215</a></span>&#160;    <span class="keywordtype">long</span>  <a class="code" href="struct_beagle_resource.html#a84d561923dd65e9bec5a22f2e782a89d">requiredFlags</a>;</div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;} <a class="code" href="struct_beagle_resource.html">BeagleResource</a>;</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;</div>
<div class="line"><a name="l00221"></a><span class="lineno"><a class="line" href="struct_beagle_resource_list.html">  221</a></span>&#160;<span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
<div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="struct_beagle_resource_list.html#aa3e1fb5c367e9f97a17f7b4ef4382dc1">  222</a></span>&#160;    <a class="code" href="struct_beagle_resource.html">BeagleResource</a>* <a class="code" href="struct_beagle_resource_list.html#aa3e1fb5c367e9f97a17f7b4ef4382dc1">list</a>; </div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="struct_beagle_resource_list.html#a8222638799bbbe0ff59bd7f89f5abbdc">  223</a></span>&#160;    <span class="keywordtype">int</span> <a class="code" href="struct_beagle_resource_list.html#a8222638799bbbe0ff59bd7f89f5abbdc">length</a>;     </div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;} <a class="code" href="struct_beagle_resource_list.html">BeagleResourceList</a>;</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;<span class="comment">/* using C calling conventions so that C programs can successfully link the beagle library</span></div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;<span class="comment"> * (brace is closed at the end of this file)</span></div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;<span class="comment"> */</span></div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;<span class="preprocessor">#ifdef __cplusplus</span></div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;<span class="preprocessor"></span><span class="keyword">extern</span> <span class="stringliteral">&quot;C&quot;</span> {</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;BEAGLE_DLLEXPORT <span class="keyword">const</span> <span class="keywordtype">char</span>* <a class="code" href="beagle_8h.html#a7548767f2cb3af22eeaec53033b826e7">beagleGetVersion</a>(<span class="keywordtype">void</span>);</div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;BEAGLE_DLLEXPORT <span class="keyword">const</span> <span class="keywordtype">char</span>* <a class="code" href="beagle_8h.html#aa057301859e993ba24d5b9fdc7f7ecd8">beagleGetCitation</a>(<span class="keywordtype">void</span>);</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;BEAGLE_DLLEXPORT <a class="code" href="struct_beagle_resource_list.html">BeagleResourceList</a>* <a class="code" href="beagle_8h.html#a389ba7c4a2e4ec083fada4b43d15df16">beagleGetResourceList</a>(<span class="keywordtype">void</span>);</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;<span class="comment">// TODO: if setting your own matrices, might not need eigen buffers allocated, but still need</span></div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;<span class="comment">//        category weight and state frequency buffers</span></div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a8bbfa8c48d0cd2dbc8f253a51f5b777e">beagleCreateInstance</a>(<span class="keywordtype">int</span> tipCount,</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;                         <span class="keywordtype">int</span> partialsBufferCount,</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;                         <span class="keywordtype">int</span> compactBufferCount,</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;                         <span class="keywordtype">int</span> stateCount,</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;                         <span class="keywordtype">int</span> patternCount,</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;                         <span class="keywordtype">int</span> eigenBufferCount,</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;                         <span class="keywordtype">int</span> matrixBufferCount,</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;                         <span class="keywordtype">int</span> categoryCount,</div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;                         <span class="keywordtype">int</span> scaleBufferCount,</div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;                         <span class="keywordtype">int</span>* resourceList,</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;                         <span class="keywordtype">int</span> resourceCount,</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;                         <span class="keywordtype">long</span> preferenceFlags,</div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;                         <span class="keywordtype">long</span> requirementFlags,</div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;                         <a class="code" href="struct_beagle_instance_details.html">BeagleInstanceDetails</a>* returnInfo);</div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;</div>
<div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#aa35df026165d96afb3a09079126666dc">beagleFinalizeInstance</a>(<span class="keywordtype">int</span> instance);</div>
<div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;</div>
<div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a7c5d6a18112618e6e4955d7f7dc22617">beagleFinalize</a>(<span class="keywordtype">void</span>);</div>
<div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;        </div>
<div class="line"><a name="l00343"></a><span class="lineno">  343</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a248ac2d4e93da19d4598a488545beb3a">beagleSetTipStates</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00344"></a><span class="lineno">  344</span>&#160;                       <span class="keywordtype">int</span> tipIndex,</div>
<div class="line"><a name="l00345"></a><span class="lineno">  345</span>&#160;                       <span class="keyword">const</span> <span class="keywordtype">int</span>* inStates);</div>
<div class="line"><a name="l00346"></a><span class="lineno">  346</span>&#160;</div>
<div class="line"><a name="l00361"></a><span class="lineno">  361</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a8da6fcc385325ac71c0268ba49c91735">beagleSetTipPartials</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00362"></a><span class="lineno">  362</span>&#160;                         <span class="keywordtype">int</span> tipIndex,</div>
<div class="line"><a name="l00363"></a><span class="lineno">  363</span>&#160;                         <span class="keyword">const</span> <span class="keywordtype">double</span>* inPartials);</div>
<div class="line"><a name="l00364"></a><span class="lineno">  364</span>&#160;</div>
<div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a4d9587451dddf791c2b28de95b91a8aa">beagleSetPartials</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;                      <span class="keywordtype">int</span> bufferIndex,</div>
<div class="line"><a name="l00379"></a><span class="lineno">  379</span>&#160;                      <span class="keyword">const</span> <span class="keywordtype">double</span>* inPartials);</div>
<div class="line"><a name="l00380"></a><span class="lineno">  380</span>&#160;</div>
<div class="line"><a name="l00394"></a><span class="lineno">  394</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a6f698c0acaf059732079e854682ab8bb">beagleGetPartials</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00395"></a><span class="lineno">  395</span>&#160;                      <span class="keywordtype">int</span> bufferIndex,</div>
<div class="line"><a name="l00396"></a><span class="lineno">  396</span>&#160;                      <span class="keywordtype">int</span> scaleIndex,</div>
<div class="line"><a name="l00397"></a><span class="lineno">  397</span>&#160;                      <span class="keywordtype">double</span>* outPartials);</div>
<div class="line"><a name="l00398"></a><span class="lineno">  398</span>&#160;</div>
<div class="line"><a name="l00413"></a><span class="lineno">  413</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#aae27b7b658d2a30a520190915ac10ae3">beagleSetEigenDecomposition</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00414"></a><span class="lineno">  414</span>&#160;                                <span class="keywordtype">int</span> eigenIndex,</div>
<div class="line"><a name="l00415"></a><span class="lineno">  415</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">double</span>* inEigenVectors,</div>
<div class="line"><a name="l00416"></a><span class="lineno">  416</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">double</span>* inInverseEigenVectors,</div>
<div class="line"><a name="l00417"></a><span class="lineno">  417</span>&#160;                                <span class="keyword">const</span> <span class="keywordtype">double</span>* inEigenValues);</div>
<div class="line"><a name="l00418"></a><span class="lineno">  418</span>&#160;</div>
<div class="line"><a name="l00430"></a><span class="lineno">  430</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#aed8f0f07b5510150efe1b72df2270f4d">beagleSetStateFrequencies</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00431"></a><span class="lineno">  431</span>&#160;                                         <span class="keywordtype">int</span> stateFrequenciesIndex,</div>
<div class="line"><a name="l00432"></a><span class="lineno">  432</span>&#160;                                         <span class="keyword">const</span> <span class="keywordtype">double</span>* inStateFrequencies);    </div>
<div class="line"><a name="l00433"></a><span class="lineno">  433</span>&#160;    </div>
<div class="line"><a name="l00445"></a><span class="lineno">  445</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a9e162e36113dfd5edb1dc57c2e99e3b5">beagleSetCategoryWeights</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00446"></a><span class="lineno">  446</span>&#160;                                        <span class="keywordtype">int</span> categoryWeightsIndex,</div>
<div class="line"><a name="l00447"></a><span class="lineno">  447</span>&#160;                                        <span class="keyword">const</span> <span class="keywordtype">double</span>* inCategoryWeights);</div>
<div class="line"><a name="l00448"></a><span class="lineno">  448</span>&#160;</div>
<div class="line"><a name="l00459"></a><span class="lineno">  459</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a404a18af42b3eb11d1d7dc8c86204ce8">beagleSetCategoryRates</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00460"></a><span class="lineno">  460</span>&#160;                           <span class="keyword">const</span> <span class="keywordtype">double</span>* inCategoryRates);</div>
<div class="line"><a name="l00471"></a><span class="lineno">  471</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#aebbfc9e38a2dd362b0f03f29cab42ac6">beagleSetPatternWeights</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00472"></a><span class="lineno">  472</span>&#160;                                       <span class="keyword">const</span> <span class="keywordtype">double</span>* inPatternWeights);</div>
<div class="line"><a name="l00473"></a><span class="lineno">  473</span>&#160;    </div>
<div class="line"><a name="l00474"></a><span class="lineno">  474</span>&#160;</div>
<div class="line"><a name="l00476"></a><span class="lineno">  476</span>&#160;<span class="comment">//---TODO: Epoch model---//</span></div>
<div class="line"><a name="l00478"></a><span class="lineno">  478</span>&#160;<span class="comment"></span></div>
<div class="line"><a name="l00493"></a><span class="lineno">  493</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a50aff3cb6241e9fe59a0cb5c5cc29ee0">beagleConvolveTransitionMatrices</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00494"></a><span class="lineno">  494</span>&#160;                                    <span class="keyword">const</span> <span class="keywordtype">int</span>* firstIndices,</div>
<div class="line"><a name="l00495"></a><span class="lineno">  495</span>&#160;                                    <span class="keyword">const</span> <span class="keywordtype">int</span>* secondIndices,</div>
<div class="line"><a name="l00496"></a><span class="lineno">  496</span>&#160;                                    <span class="keyword">const</span> <span class="keywordtype">int</span>* resultIndices,</div>
<div class="line"><a name="l00497"></a><span class="lineno">  497</span>&#160;                                            <span class="keywordtype">int</span> matrixCount);</div>
<div class="line"><a name="l00498"></a><span class="lineno">  498</span>&#160;</div>
<div class="line"><a name="l00518"></a><span class="lineno">  518</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a5528ac9d57faaa14947260a297496269">beagleUpdateTransitionMatrices</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00519"></a><span class="lineno">  519</span>&#160;                                   <span class="keywordtype">int</span> eigenIndex,</div>
<div class="line"><a name="l00520"></a><span class="lineno">  520</span>&#160;                                   <span class="keyword">const</span> <span class="keywordtype">int</span>* probabilityIndices,</div>
<div class="line"><a name="l00521"></a><span class="lineno">  521</span>&#160;                                   <span class="keyword">const</span> <span class="keywordtype">int</span>* firstDerivativeIndices,</div>
<div class="line"><a name="l00522"></a><span class="lineno">  522</span>&#160;                                   <span class="keyword">const</span> <span class="keywordtype">int</span>* secondDerivativeIndices,</div>
<div class="line"><a name="l00523"></a><span class="lineno">  523</span>&#160;                                   <span class="keyword">const</span> <span class="keywordtype">double</span>* edgeLengths,</div>
<div class="line"><a name="l00524"></a><span class="lineno">  524</span>&#160;                                   <span class="keywordtype">int</span> count);</div>
<div class="line"><a name="l00525"></a><span class="lineno">  525</span>&#160;</div>
<div class="line"><a name="l00541"></a><span class="lineno">  541</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#ac209b67480022546bed413034bf771a0">beagleSetTransitionMatrix</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00542"></a><span class="lineno">  542</span>&#160;                              <span class="keywordtype">int</span> matrixIndex,</div>
<div class="line"><a name="l00543"></a><span class="lineno">  543</span>&#160;                              <span class="keyword">const</span> <span class="keywordtype">double</span>* inMatrix,</div>
<div class="line"><a name="l00544"></a><span class="lineno">  544</span>&#160;                              <span class="keywordtype">double</span> paddedValue);</div>
<div class="line"><a name="l00545"></a><span class="lineno">  545</span>&#160;</div>
<div class="line"><a name="l00559"></a><span class="lineno">  559</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a4054c89db17dd5cc50c0f1c077bee8c8">beagleGetTransitionMatrix</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00560"></a><span class="lineno">  560</span>&#160;                                                                <span class="keywordtype">int</span> matrixIndex,</div>
<div class="line"><a name="l00561"></a><span class="lineno">  561</span>&#160;                                                                <span class="keywordtype">double</span>* outMatrix);</div>
<div class="line"><a name="l00562"></a><span class="lineno">  562</span>&#160;    </div>
<div class="line"><a name="l00579"></a><span class="lineno">  579</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a72c7aac15b0cc06f03e6177ad0a161e6">beagleSetTransitionMatrices</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00580"></a><span class="lineno">  580</span>&#160;                                                 <span class="keyword">const</span> <span class="keywordtype">int</span>* matrixIndices,</div>
<div class="line"><a name="l00581"></a><span class="lineno">  581</span>&#160;                                                 <span class="keyword">const</span> <span class="keywordtype">double</span>* inMatrices,</div>
<div class="line"><a name="l00582"></a><span class="lineno">  582</span>&#160;                                                 <span class="keyword">const</span> <span class="keywordtype">double</span>* paddedValues,</div>
<div class="line"><a name="l00583"></a><span class="lineno">  583</span>&#160;                                                 <span class="keywordtype">int</span> count);</div>
<div class="line"><a name="l00584"></a><span class="lineno">  584</span>&#160;</div>
<div class="line"><a name="l00585"></a><span class="lineno">  585</span>&#160;    </div>
<div class="line"><a name="l00589"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html">  589</a></span>&#160;<span class="keyword">typedef</span> <span class="keyword">struct </span>{</div>
<div class="line"><a name="l00590"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html#a7b71c663c3ebcd2fd1bcfcc1862cca51">  590</a></span>&#160;        <span class="keywordtype">int</span> <a class="code" href="struct_beagle_operation.html#a7b71c663c3ebcd2fd1bcfcc1862cca51">destinationPartials</a>;    </div>
<div class="line"><a name="l00591"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html#a0e51bf8a58fbb2d25a5fff1d4baa39b7">  591</a></span>&#160;        <span class="keywordtype">int</span> <a class="code" href="struct_beagle_operation.html#a0e51bf8a58fbb2d25a5fff1d4baa39b7">destinationScaleWrite</a>;  </div>
<div class="line"><a name="l00592"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html#aa43026ee69fb4af3784704e6ca558708">  592</a></span>&#160;        <span class="keywordtype">int</span> <a class="code" href="struct_beagle_operation.html#aa43026ee69fb4af3784704e6ca558708">destinationScaleRead</a>;   </div>
<div class="line"><a name="l00593"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html#ae80b315980030978f57669f626d6c5b4">  593</a></span>&#160;        <span class="keywordtype">int</span> <a class="code" href="struct_beagle_operation.html#ae80b315980030978f57669f626d6c5b4">child1Partials</a>;         </div>
<div class="line"><a name="l00594"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html#a7131c3cfedd5f11b3cec4f609656aeba">  594</a></span>&#160;        <span class="keywordtype">int</span> <a class="code" href="struct_beagle_operation.html#a7131c3cfedd5f11b3cec4f609656aeba">child1TransitionMatrix</a>; </div>
<div class="line"><a name="l00595"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html#a089fa039ed17741a66e82a486985a3df">  595</a></span>&#160;        <span class="keywordtype">int</span> <a class="code" href="struct_beagle_operation.html#a089fa039ed17741a66e82a486985a3df">child2Partials</a>;         </div>
<div class="line"><a name="l00596"></a><span class="lineno"><a class="line" href="struct_beagle_operation.html#adb294270f71d2e17653240f4de325f4c">  596</a></span>&#160;        <span class="keywordtype">int</span> <a class="code" href="struct_beagle_operation.html#adb294270f71d2e17653240f4de325f4c">child2TransitionMatrix</a>; </div>
<div class="line"><a name="l00597"></a><span class="lineno">  597</span>&#160;} <a class="code" href="struct_beagle_operation.html">BeagleOperation</a>;</div>
<div class="line"><a name="l00598"></a><span class="lineno">  598</span>&#160;</div>
<div class="line"><a name="l00613"></a><span class="lineno">  613</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a1c6335b5efc17f331282daec82e94226">beagleUpdatePartials</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00614"></a><span class="lineno">  614</span>&#160;                         <span class="keyword">const</span> <a class="code" href="struct_beagle_operation.html">BeagleOperation</a>* operations,</div>
<div class="line"><a name="l00615"></a><span class="lineno">  615</span>&#160;                         <span class="keywordtype">int</span> operationCount,</div>
<div class="line"><a name="l00616"></a><span class="lineno">  616</span>&#160;                         <span class="keywordtype">int</span> cumulativeScaleIndex);</div>
<div class="line"><a name="l00617"></a><span class="lineno">  617</span>&#160;</div>
<div class="line"><a name="l00634"></a><span class="lineno">  634</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#ab34345b9feb1a92a9ed247dbb93192b4">beagleWaitForPartials</a>(<span class="keyword">const</span> <span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00635"></a><span class="lineno">  635</span>&#160;                          <span class="keyword">const</span> <span class="keywordtype">int</span>* destinationPartials,</div>
<div class="line"><a name="l00636"></a><span class="lineno">  636</span>&#160;                          <span class="keywordtype">int</span> destinationPartialsCount);</div>
<div class="line"><a name="l00637"></a><span class="lineno">  637</span>&#160;</div>
<div class="line"><a name="l00649"></a><span class="lineno">  649</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#aea0ba5ba75cda49363b82f48def77847">beagleAccumulateScaleFactors</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00650"></a><span class="lineno">  650</span>&#160;                                 <span class="keyword">const</span> <span class="keywordtype">int</span>* scaleIndices,</div>
<div class="line"><a name="l00651"></a><span class="lineno">  651</span>&#160;                                 <span class="keywordtype">int</span> count,</div>
<div class="line"><a name="l00652"></a><span class="lineno">  652</span>&#160;                                 <span class="keywordtype">int</span> cumulativeScaleIndex);</div>
<div class="line"><a name="l00653"></a><span class="lineno">  653</span>&#160;</div>
<div class="line"><a name="l00665"></a><span class="lineno">  665</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a0703dedf208d98a4b86ea8ee0b2e358d">beagleRemoveScaleFactors</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00666"></a><span class="lineno">  666</span>&#160;                             <span class="keyword">const</span> <span class="keywordtype">int</span>* scaleIndices,</div>
<div class="line"><a name="l00667"></a><span class="lineno">  667</span>&#160;                             <span class="keywordtype">int</span> count,</div>
<div class="line"><a name="l00668"></a><span class="lineno">  668</span>&#160;                             <span class="keywordtype">int</span> cumulativeScaleIndex);</div>
<div class="line"><a name="l00669"></a><span class="lineno">  669</span>&#160;</div>
<div class="line"><a name="l00678"></a><span class="lineno">  678</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#ad0b1d6509865e06715cf96b7f5ec0b13">beagleResetScaleFactors</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00679"></a><span class="lineno">  679</span>&#160;                            <span class="keywordtype">int</span> cumulativeScaleIndex);</div>
<div class="line"><a name="l00680"></a><span class="lineno">  680</span>&#160;</div>
<div class="line"><a name="l00690"></a><span class="lineno">  690</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a66c460f21b89acb0ad551be0d9143133">beagleCopyScaleFactors</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00691"></a><span class="lineno">  691</span>&#160;                                            <span class="keywordtype">int</span> destScalingIndex,</div>
<div class="line"><a name="l00692"></a><span class="lineno">  692</span>&#160;                                            <span class="keywordtype">int</span> srcScalingIndex);</div>
<div class="line"><a name="l00693"></a><span class="lineno">  693</span>&#160;    </div>
<div class="line"><a name="l00715"></a><span class="lineno">  715</span>&#160;<span class="comment">// TODO: only need one state frequency index</span></div>
<div class="line"><a name="l00716"></a><span class="lineno">  716</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a967f3d7704eb53e34b091b86a7e9baee">beagleCalculateRootLogLikelihoods</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00717"></a><span class="lineno">  717</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* bufferIndices,</div>
<div class="line"><a name="l00718"></a><span class="lineno">  718</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* categoryWeightsIndices,</div>
<div class="line"><a name="l00719"></a><span class="lineno">  719</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* stateFrequenciesIndices,</div>
<div class="line"><a name="l00720"></a><span class="lineno">  720</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* cumulativeScaleIndices,</div>
<div class="line"><a name="l00721"></a><span class="lineno">  721</span>&#160;                                      <span class="keywordtype">int</span> count,</div>
<div class="line"><a name="l00722"></a><span class="lineno">  722</span>&#160;                                      <span class="keywordtype">double</span>* outSumLogLikelihood);</div>
<div class="line"><a name="l00723"></a><span class="lineno">  723</span>&#160;</div>
<div class="line"><a name="l00751"></a><span class="lineno">  751</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a1622661032ea7959e985592d86a9fa77">beagleCalculateEdgeLogLikelihoods</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00752"></a><span class="lineno">  752</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* parentBufferIndices,</div>
<div class="line"><a name="l00753"></a><span class="lineno">  753</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* childBufferIndices,</div>
<div class="line"><a name="l00754"></a><span class="lineno">  754</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* probabilityIndices,</div>
<div class="line"><a name="l00755"></a><span class="lineno">  755</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* firstDerivativeIndices,</div>
<div class="line"><a name="l00756"></a><span class="lineno">  756</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* secondDerivativeIndices,</div>
<div class="line"><a name="l00757"></a><span class="lineno">  757</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* categoryWeightsIndices,</div>
<div class="line"><a name="l00758"></a><span class="lineno">  758</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* stateFrequenciesIndices,</div>
<div class="line"><a name="l00759"></a><span class="lineno">  759</span>&#160;                                      <span class="keyword">const</span> <span class="keywordtype">int</span>* cumulativeScaleIndices,</div>
<div class="line"><a name="l00760"></a><span class="lineno">  760</span>&#160;                                      <span class="keywordtype">int</span> count,</div>
<div class="line"><a name="l00761"></a><span class="lineno">  761</span>&#160;                                      <span class="keywordtype">double</span>* outSumLogLikelihood,</div>
<div class="line"><a name="l00762"></a><span class="lineno">  762</span>&#160;                                      <span class="keywordtype">double</span>* outSumFirstDerivative,</div>
<div class="line"><a name="l00763"></a><span class="lineno">  763</span>&#160;                                      <span class="keywordtype">double</span>* outSumSecondDerivative);</div>
<div class="line"><a name="l00764"></a><span class="lineno">  764</span>&#160;</div>
<div class="line"><a name="l00776"></a><span class="lineno">  776</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a8de7a453b2d4a89be02f75f8e9ae9ab9">beagleGetSiteLogLikelihoods</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00777"></a><span class="lineno">  777</span>&#160;                                       <span class="keywordtype">double</span>* outLogLikelihoods);</div>
<div class="line"><a name="l00778"></a><span class="lineno">  778</span>&#160;</div>
<div class="line"><a name="l00790"></a><span class="lineno">  790</span>&#160;BEAGLE_DLLEXPORT <span class="keywordtype">int</span> <a class="code" href="beagle_8h.html#a7bd7856124724dc18058935d8aaa08ec">beagleGetSiteDerivatives</a>(<span class="keywordtype">int</span> instance,</div>
<div class="line"><a name="l00791"></a><span class="lineno">  791</span>&#160;                                    <span class="keywordtype">double</span>* outFirstDerivatives,</div>
<div class="line"><a name="l00792"></a><span class="lineno">  792</span>&#160;                                    <span class="keywordtype">double</span>* outSecondDerivatives);    </div>
<div class="line"><a name="l00793"></a><span class="lineno">  793</span>&#160;    </div>
<div class="line"><a name="l00794"></a><span class="lineno">  794</span>&#160;<span class="comment">/* using C calling conventions so that C programs can successfully link the beagle library</span></div>
<div class="line"><a name="l00795"></a><span class="lineno">  795</span>&#160;<span class="comment"> * (closing brace)</span></div>
<div class="line"><a name="l00796"></a><span class="lineno">  796</span>&#160;<span class="comment"> */</span></div>
<div class="line"><a name="l00797"></a><span class="lineno">  797</span>&#160;<span class="preprocessor">#ifdef __cplusplus</span></div>
<div class="line"><a name="l00798"></a><span class="lineno">  798</span>&#160;<span class="preprocessor"></span>}</div>
<div class="line"><a name="l00799"></a><span class="lineno">  799</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00800"></a><span class="lineno">  800</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00801"></a><span class="lineno">  801</span>&#160;<span class="preprocessor">#endif // __beagle__</span></div>
<div class="ttc" id="beagle_8h_html_a7548767f2cb3af22eeaec53033b826e7"><div class="ttname"><a href="beagle_8h.html#a7548767f2cb3af22eeaec53033b826e7">beagleGetVersion</a></div><div class="ttdeci">BEAGLE_DLLEXPORT const char * beagleGetVersion(void)</div><div class="ttdoc">Get version. </div></div>
<div class="ttc" id="beagle_8h_html_a404a18af42b3eb11d1d7dc8c86204ce8"><div class="ttname"><a href="beagle_8h.html#a404a18af42b3eb11d1d7dc8c86204ce8">beagleSetCategoryRates</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetCategoryRates(int instance, const double *inCategoryRates)</div><div class="ttdoc">Set category rates. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeac2cf9217aa4e7a2e002746528a8ba29b"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac2cf9217aa4e7a2e002746528a8ba29b">BEAGLE_FLAG_COMPUTATION_ASYNCH</a></div><div class="ttdef"><b>Definition:</b> beagle.h:147</div></div>
<div class="ttc" id="beagle_8h_html_a2487a1c99f4214cd3a70468d0ccac55ca907d2c6aac07be265a496476a55216e5"><div class="ttname"><a href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55ca907d2c6aac07be265a496476a55216e5">BEAGLE_OP_COUNT</a></div><div class="ttdef"><b>Definition:</b> beagle.h:190</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeac522542d33f45928656aa2dfe478b3ce"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac522542d33f45928656aa2dfe478b3ce">BEAGLE_FLAG_THREADING_OPENMP</a></div><div class="ttdef"><b>Definition:</b> beagle.h:167</div></div>
<div class="ttc" id="struct_beagle_instance_details_html_a05420095a96892a7da9ca33ec737c4a2"><div class="ttname"><a href="struct_beagle_instance_details.html#a05420095a96892a7da9ca33ec737c4a2">BeagleInstanceDetails::implName</a></div><div class="ttdeci">char * implName</div><div class="ttdef"><b>Definition:</b> beagle.h:201</div></div>
<div class="ttc" id="struct_beagle_resource_list_html"><div class="ttname"><a href="struct_beagle_resource_list.html">BeagleResourceList</a></div><div class="ttdoc">List of hardware resources. </div><div class="ttdef"><b>Definition:</b> beagle.h:221</div></div>
<div class="ttc" id="struct_beagle_operation_html_ae80b315980030978f57669f626d6c5b4"><div class="ttname"><a href="struct_beagle_operation.html#ae80b315980030978f57669f626d6c5b4">BeagleOperation::child1Partials</a></div><div class="ttdeci">int child1Partials</div><div class="ttdef"><b>Definition:</b> beagle.h:593</div></div>
<div class="ttc" id="struct_beagle_resource_html_a84d561923dd65e9bec5a22f2e782a89d"><div class="ttname"><a href="struct_beagle_resource.html#a84d561923dd65e9bec5a22f2e782a89d">BeagleResource::requiredFlags</a></div><div class="ttdeci">long requiredFlags</div><div class="ttdef"><b>Definition:</b> beagle.h:215</div></div>
<div class="ttc" id="beagle_8h_html_aae27b7b658d2a30a520190915ac10ae3"><div class="ttname"><a href="beagle_8h.html#aae27b7b658d2a30a520190915ac10ae3">beagleSetEigenDecomposition</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetEigenDecomposition(int instance, int eigenIndex, const double *inEigenVectors, const double *inInverseEigenVectors, const double *inEigenValues)</div><div class="ttdoc">Set an eigen-decomposition buffer. </div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfcea74be6f002aba021c7093dfe50b44f1ed"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea74be6f002aba021c7093dfe50b44f1ed">BEAGLE_ERROR_NO_IMPLEMENTATION</a></div><div class="ttdef"><b>Definition:</b> beagle.h:130</div></div>
<div class="ttc" id="beagle_8h_html_a2487a1c99f4214cd3a70468d0ccac55ca2eb262bbe41b1dbeff3e189d8de65b04"><div class="ttname"><a href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55ca2eb262bbe41b1dbeff3e189d8de65b04">BEAGLE_OP_NONE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:191</div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfceaec9b03ad5cd754a99ed84e1755704beb"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaec9b03ad5cd754a99ed84e1755704beb">BEAGLE_ERROR_NO_RESOURCE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:129</div></div>
<div class="ttc" id="struct_beagle_instance_details_html"><div class="ttname"><a href="struct_beagle_instance_details.html">BeagleInstanceDetails</a></div><div class="ttdoc">Information about a specific instance. </div><div class="ttdef"><b>Definition:</b> beagle.h:197</div></div>
<div class="ttc" id="struct_beagle_operation_html_aa43026ee69fb4af3784704e6ca558708"><div class="ttname"><a href="struct_beagle_operation.html#aa43026ee69fb4af3784704e6ca558708">BeagleOperation::destinationScaleRead</a></div><div class="ttdeci">int destinationScaleRead</div><div class="ttdef"><b>Definition:</b> beagle.h:592</div></div>
<div class="ttc" id="struct_beagle_resource_html_a529ec0036f2af507febd15940dc0575b"><div class="ttname"><a href="struct_beagle_resource.html#a529ec0036f2af507febd15940dc0575b">BeagleResource::description</a></div><div class="ttdeci">char * description</div><div class="ttdef"><b>Definition:</b> beagle.h:213</div></div>
<div class="ttc" id="beagle_8h_html_a2487a1c99f4214cd3a70468d0ccac55c"><div class="ttname"><a href="beagle_8h.html#a2487a1c99f4214cd3a70468d0ccac55c">BeagleOpCodes</a></div><div class="ttdeci">BeagleOpCodes</div><div class="ttdoc">Operation codes. </div><div class="ttdef"><b>Definition:</b> beagle.h:189</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea6f9a787ae342115c27a7437e8b0d9dc6"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea6f9a787ae342115c27a7437e8b0d9dc6">BEAGLE_FLAG_VECTOR_SSE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:163</div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfceaf31bb198b162f0d9ed2e0490a475409d"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaf31bb198b162f0d9ed2e0490a475409d">BEAGLE_ERROR_OUT_OF_MEMORY</a></div><div class="ttdef"><b>Definition:</b> beagle.h:123</div></div>
<div class="ttc" id="struct_beagle_resource_html_a114a8e272a9b10d6e2b1629c3ba62fcd"><div class="ttname"><a href="struct_beagle_resource.html#a114a8e272a9b10d6e2b1629c3ba62fcd">BeagleResource::supportFlags</a></div><div class="ttdeci">long supportFlags</div><div class="ttdef"><b>Definition:</b> beagle.h:214</div></div>
<div class="ttc" id="struct_beagle_resource_list_html_a8222638799bbbe0ff59bd7f89f5abbdc"><div class="ttname"><a href="struct_beagle_resource_list.html#a8222638799bbbe0ff59bd7f89f5abbdc">BeagleResourceList::length</a></div><div class="ttdeci">int length</div><div class="ttdef"><b>Definition:</b> beagle.h:223</div></div>
<div class="ttc" id="beagle_8h_html_a4d9587451dddf791c2b28de95b91a8aa"><div class="ttname"><a href="beagle_8h.html#a4d9587451dddf791c2b28de95b91a8aa">beagleSetPartials</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetPartials(int instance, int bufferIndex, const double *inPartials)</div><div class="ttdoc">Set an instance partials buffer. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeaad2f12434a5b2882925c836976cf49cc"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeaad2f12434a5b2882925c836976cf49cc">BEAGLE_FLAG_PROCESSOR_PHI</a></div><div class="ttdef"><b>Definition:</b> beagle.h:174</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea3e2ddc258bd1d83c75bbeff3f57c94d8"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea3e2ddc258bd1d83c75bbeff3f57c94d8">BEAGLE_FLAG_PROCESSOR_OTHER</a></div><div class="ttdef"><b>Definition:</b> beagle.h:175</div></div>
<div class="ttc" id="beagle_8h_html_a1622661032ea7959e985592d86a9fa77"><div class="ttname"><a href="beagle_8h.html#a1622661032ea7959e985592d86a9fa77">beagleCalculateEdgeLogLikelihoods</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleCalculateEdgeLogLikelihoods(int instance, const int *parentBufferIndices, const int *childBufferIndices, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood, double *outSumFirstDerivative, double *outSumSecondDerivative)</div><div class="ttdoc">Calculate site log likelihoods and derivatives along an edge. </div></div>
<div class="ttc" id="beagle_8h_html_a4054c89db17dd5cc50c0f1c077bee8c8"><div class="ttname"><a href="beagle_8h.html#a4054c89db17dd5cc50c0f1c077bee8c8">beagleGetTransitionMatrix</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleGetTransitionMatrix(int instance, int matrixIndex, double *outMatrix)</div><div class="ttdoc">Get a finite-time transition probability matrix. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea444ce15e77f6cfaeb77ee1762925cd77"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea444ce15e77f6cfaeb77ee1762925cd77">BEAGLE_FLAG_THREADING_NONE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:168</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea8c750c64eb7c532c40a1b520c7253656"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea8c750c64eb7c532c40a1b520c7253656">BEAGLE_FLAG_SCALING_DYNAMIC</a></div><div class="ttdef"><b>Definition:</b> beagle.h:155</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea538654597350cea65553c70189ceb107"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea538654597350cea65553c70189ceb107">BEAGLE_FLAG_VECTOR_NONE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:165</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeacc951e8ceb79f83b91977b2cea646917"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeacc951e8ceb79f83b91977b2cea646917">BEAGLE_FLAG_FRAMEWORK_CPU</a></div><div class="ttdef"><b>Definition:</b> beagle.h:179</div></div>
<div class="ttc" id="beagle_8h_html_a6f698c0acaf059732079e854682ab8bb"><div class="ttname"><a href="beagle_8h.html#a6f698c0acaf059732079e854682ab8bb">beagleGetPartials</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleGetPartials(int instance, int bufferIndex, int scaleIndex, double *outPartials)</div><div class="ttdoc">Get partials from an instance buffer. </div></div>
<div class="ttc" id="beagle_8h_html_ac209b67480022546bed413034bf771a0"><div class="ttname"><a href="beagle_8h.html#ac209b67480022546bed413034bf771a0">beagleSetTransitionMatrix</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetTransitionMatrix(int instance, int matrixIndex, const double *inMatrix, double paddedValue)</div><div class="ttdoc">Set a finite-time transition probability matrix. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea9aea9b1db1765a059e5f0c994c7ff5b4"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9aea9b1db1765a059e5f0c994c7ff5b4">BEAGLE_FLAG_PROCESSOR_CPU</a></div><div class="ttdef"><b>Definition:</b> beagle.h:170</div></div>
<div class="ttc" id="struct_beagle_instance_details_html_a06dd93495752717d4a55a75b3f4452d5"><div class="ttname"><a href="struct_beagle_instance_details.html#a06dd93495752717d4a55a75b3f4452d5">BeagleInstanceDetails::implDescription</a></div><div class="ttdeci">char * implDescription</div><div class="ttdef"><b>Definition:</b> beagle.h:203</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea96ef202a6ec8fc3754dc3095b30a87fb"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea96ef202a6ec8fc3754dc3095b30a87fb">BEAGLE_FLAG_EIGEN_REAL</a></div><div class="ttdef"><b>Definition:</b> beagle.h:149</div></div>
<div class="ttc" id="beagle_8h_html_a7c5d6a18112618e6e4955d7f7dc22617"><div class="ttname"><a href="beagle_8h.html#a7c5d6a18112618e6e4955d7f7dc22617">beagleFinalize</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleFinalize(void)</div><div class="ttdoc">Finalize the library. </div></div>
<div class="ttc" id="struct_beagle_operation_html_adb294270f71d2e17653240f4de325f4c"><div class="ttname"><a href="struct_beagle_operation.html#adb294270f71d2e17653240f4de325f4c">BeagleOperation::child2TransitionMatrix</a></div><div class="ttdeci">int child2TransitionMatrix</div><div class="ttdef"><b>Definition:</b> beagle.h:596</div></div>
<div class="ttc" id="struct_beagle_operation_html_a089fa039ed17741a66e82a486985a3df"><div class="ttname"><a href="struct_beagle_operation.html#a089fa039ed17741a66e82a486985a3df">BeagleOperation::child2Partials</a></div><div class="ttdeci">int child2Partials</div><div class="ttdef"><b>Definition:</b> beagle.h:595</div></div>
<div class="ttc" id="beagle_8h_html_aea0ba5ba75cda49363b82f48def77847"><div class="ttname"><a href="beagle_8h.html#aea0ba5ba75cda49363b82f48def77847">beagleAccumulateScaleFactors</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleAccumulateScaleFactors(int instance, const int *scaleIndices, int count, int cumulativeScaleIndex)</div><div class="ttdoc">Accumulate scale factors. </div></div>
<div class="ttc" id="struct_beagle_instance_details_html_a2f95e32bd70ddef33d3676673e1403ff"><div class="ttname"><a href="struct_beagle_instance_details.html#a2f95e32bd70ddef33d3676673e1403ff">BeagleInstanceDetails::resourceName</a></div><div class="ttdeci">char * resourceName</div><div class="ttdef"><b>Definition:</b> beagle.h:199</div></div>
<div class="ttc" id="struct_beagle_instance_details_html_a73d2211c0f0d5b730d7a768155ff0be4"><div class="ttname"><a href="struct_beagle_instance_details.html#a73d2211c0f0d5b730d7a768155ff0be4">BeagleInstanceDetails::flags</a></div><div class="ttdeci">long flags</div><div class="ttdef"><b>Definition:</b> beagle.h:204</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea44746eb12a08bd5427ecf7e0508e02e9"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea44746eb12a08bd5427ecf7e0508e02e9">BEAGLE_FLAG_SCALING_MANUAL</a></div><div class="ttdef"><b>Definition:</b> beagle.h:152</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea11d8bbb56c0d104bf29e877f90f12935"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea11d8bbb56c0d104bf29e877f90f12935">BEAGLE_FLAG_SCALING_ALWAYS</a></div><div class="ttdef"><b>Definition:</b> beagle.h:154</div></div>
<div class="ttc" id="struct_beagle_operation_html_a7131c3cfedd5f11b3cec4f609656aeba"><div class="ttname"><a href="struct_beagle_operation.html#a7131c3cfedd5f11b3cec4f609656aeba">BeagleOperation::child1TransitionMatrix</a></div><div class="ttdeci">int child1TransitionMatrix</div><div class="ttdef"><b>Definition:</b> beagle.h:594</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea5dcb70fa15d216e8295982953d535ff9"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea5dcb70fa15d216e8295982953d535ff9">BEAGLE_FLAG_PROCESSOR_CELL</a></div><div class="ttdef"><b>Definition:</b> beagle.h:173</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeab55cd0f09a8c91e5d2d51b239515da4a"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeab55cd0f09a8c91e5d2d51b239515da4a">BEAGLE_FLAG_VECTOR_AVX</a></div><div class="ttdef"><b>Definition:</b> beagle.h:164</div></div>
<div class="ttc" id="struct_beagle_resource_list_html_aa3e1fb5c367e9f97a17f7b4ef4382dc1"><div class="ttname"><a href="struct_beagle_resource_list.html#aa3e1fb5c367e9f97a17f7b4ef4382dc1">BeagleResourceList::list</a></div><div class="ttdeci">BeagleResource * list</div><div class="ttdef"><b>Definition:</b> beagle.h:222</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeac4e28e01f5d95262033f72410ca57c89"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeac4e28e01f5d95262033f72410ca57c89">BEAGLE_FLAG_COMPUTATION_SYNCH</a></div><div class="ttdef"><b>Definition:</b> beagle.h:146</div></div>
<div class="ttc" id="beagle_8h_html_ab34345b9feb1a92a9ed247dbb93192b4"><div class="ttname"><a href="beagle_8h.html#ab34345b9feb1a92a9ed247dbb93192b4">beagleWaitForPartials</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleWaitForPartials(const int instance, const int *destinationPartials, int destinationPartialsCount)</div><div class="ttdoc">Block until all calculations that write to the specified partials have completed. ...</div></div>
<div class="ttc" id="beagle_8h_html_aa057301859e993ba24d5b9fdc7f7ecd8"><div class="ttname"><a href="beagle_8h.html#aa057301859e993ba24d5b9fdc7f7ecd8">beagleGetCitation</a></div><div class="ttdeci">BEAGLE_DLLEXPORT const char * beagleGetCitation(void)</div><div class="ttdoc">Get citation. </div></div>
<div class="ttc" id="beagle_8h_html_a9e162e36113dfd5edb1dc57c2e99e3b5"><div class="ttname"><a href="beagle_8h.html#a9e162e36113dfd5edb1dc57c2e99e3b5">beagleSetCategoryWeights</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetCategoryWeights(int instance, int categoryWeightsIndex, const double *inCategoryWeights)</div><div class="ttdoc">Set a category weights buffer. </div></div>
<div class="ttc" id="beagle_8h_html_a66c460f21b89acb0ad551be0d9143133"><div class="ttname"><a href="beagle_8h.html#a66c460f21b89acb0ad551be0d9143133">beagleCopyScaleFactors</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleCopyScaleFactors(int instance, int destScalingIndex, int srcScalingIndex)</div><div class="ttdoc">Copy scale factors. </div></div>
<div class="ttc" id="struct_beagle_instance_details_html_a62da477128f3d7d56b58a97445e5c777"><div class="ttname"><a href="struct_beagle_instance_details.html#a62da477128f3d7d56b58a97445e5c777">BeagleInstanceDetails::resourceNumber</a></div><div class="ttdeci">int resourceNumber</div><div class="ttdef"><b>Definition:</b> beagle.h:198</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea6efa1e464b74cfcf6e7317d79bf1c085"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea6efa1e464b74cfcf6e7317d79bf1c085">BEAGLE_FLAG_PRECISION_SINGLE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:143</div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfcea1118b576b6d5e1372f757ec246acd203"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea1118b576b6d5e1372f757ec246acd203">BEAGLE_ERROR_OUT_OF_RANGE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:127</div></div>
<div class="ttc" id="beagle_8h_html_a967f3d7704eb53e34b091b86a7e9baee"><div class="ttname"><a href="beagle_8h.html#a967f3d7704eb53e34b091b86a7e9baee">beagleCalculateRootLogLikelihoods</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleCalculateRootLogLikelihoods(int instance, const int *bufferIndices, const int *categoryWeightsIndices, const int *stateFrequenciesIndices, const int *cumulativeScaleIndices, int count, double *outSumLogLikelihood)</div><div class="ttdoc">Calculate site log likelihoods at a root node. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea81574eae3cca4fd42b3b34d731555b64"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea81574eae3cca4fd42b3b34d731555b64">BEAGLE_FLAG_SCALERS_RAW</a></div><div class="ttdef"><b>Definition:</b> beagle.h:157</div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfcea12aea4769c1be89867846782925b1cbe"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea12aea4769c1be89867846782925b1cbe">BEAGLE_SUCCESS</a></div><div class="ttdef"><b>Definition:</b> beagle.h:121</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea04dcbc29ff83699be424c21b38e57d06"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea04dcbc29ff83699be424c21b38e57d06">BEAGLE_FLAG_FRAMEWORK_OPENCL</a></div><div class="ttdef"><b>Definition:</b> beagle.h:178</div></div>
<div class="ttc" id="beagle_8h_html_a5528ac9d57faaa14947260a297496269"><div class="ttname"><a href="beagle_8h.html#a5528ac9d57faaa14947260a297496269">beagleUpdateTransitionMatrices</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleUpdateTransitionMatrices(int instance, int eigenIndex, const int *probabilityIndices, const int *firstDerivativeIndices, const int *secondDerivativeIndices, const double *edgeLengths, int count)</div><div class="ttdoc">Calculate a list of transition probability matrices. </div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfcea267dcbe8ced105decc94598ba2be51ba"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea267dcbe8ced105decc94598ba2be51ba">BEAGLE_ERROR_FLOATING_POINT</a></div><div class="ttdef"><b>Definition:</b> beagle.h:131</div></div>
<div class="ttc" id="beagle_8h_html_a8de7a453b2d4a89be02f75f8e9ae9ab9"><div class="ttname"><a href="beagle_8h.html#a8de7a453b2d4a89be02f75f8e9ae9ab9">beagleGetSiteLogLikelihoods</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleGetSiteLogLikelihoods(int instance, double *outLogLikelihoods)</div><div class="ttdoc">Get site log likelihoods for last beagleCalculateRootLogLikelihoods or beagleCalculateEdgeLogLikeliho...</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeadbd1b3e83d25b5fae3a14a724b24cec2"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeadbd1b3e83d25b5fae3a14a724b24cec2">BEAGLE_FLAG_INVEVEC_STANDARD</a></div><div class="ttdef"><b>Definition:</b> beagle.h:160</div></div>
<div class="ttc" id="beagle_8h_html_a1c6335b5efc17f331282daec82e94226"><div class="ttname"><a href="beagle_8h.html#a1c6335b5efc17f331282daec82e94226">beagleUpdatePartials</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleUpdatePartials(const int instance, const BeagleOperation *operations, int operationCount, int cumulativeScaleIndex)</div><div class="ttdoc">Calculate or queue for calculation partials using a list of operations. </div></div>
<div class="ttc" id="beagle_8h_html_a50aff3cb6241e9fe59a0cb5c5cc29ee0"><div class="ttname"><a href="beagle_8h.html#a50aff3cb6241e9fe59a0cb5c5cc29ee0">beagleConvolveTransitionMatrices</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleConvolveTransitionMatrices(int instance, const int *firstIndices, const int *secondIndices, const int *resultIndices, int matrixCount)</div><div class="ttdoc">Convolve lists of transition probability matrices. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea78667e7bb79ac6c002d0180d3e27d6b5"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea78667e7bb79ac6c002d0180d3e27d6b5">BEAGLE_FLAG_SCALING_AUTO</a></div><div class="ttdef"><b>Definition:</b> beagle.h:153</div></div>
<div class="ttc" id="beagle_8h_html_a8da6fcc385325ac71c0268ba49c91735"><div class="ttname"><a href="beagle_8h.html#a8da6fcc385325ac71c0268ba49c91735">beagleSetTipPartials</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetTipPartials(int instance, int tipIndex, const double *inPartials)</div><div class="ttdoc">Set an instance partials buffer for tip node. </div></div>
<div class="ttc" id="struct_beagle_operation_html_a7b71c663c3ebcd2fd1bcfcc1862cca51"><div class="ttname"><a href="struct_beagle_operation.html#a7b71c663c3ebcd2fd1bcfcc1862cca51">BeagleOperation::destinationPartials</a></div><div class="ttdeci">int destinationPartials</div><div class="ttdef"><b>Definition:</b> beagle.h:590</div></div>
<div class="ttc" id="beagle_8h_html_aa35df026165d96afb3a09079126666dc"><div class="ttname"><a href="beagle_8h.html#aa35df026165d96afb3a09079126666dc">beagleFinalizeInstance</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleFinalizeInstance(int instance)</div><div class="ttdoc">Finalize this instance. </div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfcea3fd3b3dc476c527884e6db3dc0d13738"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea3fd3b3dc476c527884e6db3dc0d13738">BEAGLE_ERROR_UNIDENTIFIED_EXCEPTION</a></div><div class="ttdef"><b>Definition:</b> beagle.h:124</div></div>
<div class="ttc" id="beagle_8h_html_aebbfc9e38a2dd362b0f03f29cab42ac6"><div class="ttname"><a href="beagle_8h.html#aebbfc9e38a2dd362b0f03f29cab42ac6">beagleSetPatternWeights</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetPatternWeights(int instance, const double *inPatternWeights)</div><div class="ttdoc">Set pattern weights. </div></div>
<div class="ttc" id="beagle_8h_html_aed8f0f07b5510150efe1b72df2270f4d"><div class="ttname"><a href="beagle_8h.html#aed8f0f07b5510150efe1b72df2270f4d">beagleSetStateFrequencies</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetStateFrequencies(int instance, int stateFrequenciesIndex, const double *inStateFrequencies)</div><div class="ttdoc">Set a state frequency buffer. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddeaf7a580b8584fbdba42c5a1bab2b6ed6c"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddeaf7a580b8584fbdba42c5a1bab2b6ed6c">BEAGLE_FLAG_PROCESSOR_GPU</a></div><div class="ttdef"><b>Definition:</b> beagle.h:171</div></div>
<div class="ttc" id="beagle_8h_html_a8bbfa8c48d0cd2dbc8f253a51f5b777e"><div class="ttname"><a href="beagle_8h.html#a8bbfa8c48d0cd2dbc8f253a51f5b777e">beagleCreateInstance</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleCreateInstance(int tipCount, int partialsBufferCount, int compactBufferCount, int stateCount, int patternCount, int eigenBufferCount, int matrixBufferCount, int categoryCount, int scaleBufferCount, int *resourceList, int resourceCount, long preferenceFlags, long requirementFlags, BeagleInstanceDetails *returnInfo)</div><div class="ttdoc">Create a single instance. </div></div>
<div class="ttc" id="struct_beagle_resource_html"><div class="ttname"><a href="struct_beagle_resource.html">BeagleResource</a></div><div class="ttdoc">Description of a hardware resource. </div><div class="ttdef"><b>Definition:</b> beagle.h:211</div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfcea45c3bd53fdd83865d927202d0d582299"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfcea45c3bd53fdd83865d927202d0d582299">BEAGLE_ERROR_GENERAL</a></div><div class="ttdef"><b>Definition:</b> beagle.h:122</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea9480c27a220b39df8980176376e27bbf"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9480c27a220b39df8980176376e27bbf">BEAGLE_FLAG_PROCESSOR_FPGA</a></div><div class="ttdef"><b>Definition:</b> beagle.h:172</div></div>
<div class="ttc" id="beagle_8h_html_a389ba7c4a2e4ec083fada4b43d15df16"><div class="ttname"><a href="beagle_8h.html#a389ba7c4a2e4ec083fada4b43d15df16">beagleGetResourceList</a></div><div class="ttdeci">BEAGLE_DLLEXPORT BeagleResourceList * beagleGetResourceList(void)</div><div class="ttdoc">Get list of hardware resources. </div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea83963bbb1062fd6c060553de8dd6b429"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea83963bbb1062fd6c060553de8dd6b429">BEAGLE_FLAG_PRECISION_DOUBLE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:144</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bdde"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bdde">BeagleFlags</a></div><div class="ttdeci">BeagleFlags</div><div class="ttdoc">Hardware and implementation capability flags. </div><div class="ttdef"><b>Definition:</b> beagle.h:142</div></div>
<div class="ttc" id="beagle_8h_html_a248ac2d4e93da19d4598a488545beb3a"><div class="ttname"><a href="beagle_8h.html#a248ac2d4e93da19d4598a488545beb3a">beagleSetTipStates</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetTipStates(int instance, int tipIndex, const int *inStates)</div><div class="ttdoc">Set the compact state representation for tip node. </div></div>
<div class="ttc" id="beagle_8h_html_a7bd7856124724dc18058935d8aaa08ec"><div class="ttname"><a href="beagle_8h.html#a7bd7856124724dc18058935d8aaa08ec">beagleGetSiteDerivatives</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleGetSiteDerivatives(int instance, double *outFirstDerivatives, double *outSecondDerivatives)</div><div class="ttdoc">Get site derivatives for last beagleCalculateEdgeLogLikelihoods call. </div></div>
<div class="ttc" id="beagle_8h_html_a0703dedf208d98a4b86ea8ee0b2e358d"><div class="ttname"><a href="beagle_8h.html#a0703dedf208d98a4b86ea8ee0b2e358d">beagleRemoveScaleFactors</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleRemoveScaleFactors(int instance, const int *scaleIndices, int count, int cumulativeScaleIndex)</div><div class="ttdoc">Remove scale factors. </div></div>
<div class="ttc" id="struct_beagle_operation_html_a0e51bf8a58fbb2d25a5fff1d4baa39b7"><div class="ttname"><a href="struct_beagle_operation.html#a0e51bf8a58fbb2d25a5fff1d4baa39b7">BeagleOperation::destinationScaleWrite</a></div><div class="ttdeci">int destinationScaleWrite</div><div class="ttdef"><b>Definition:</b> beagle.h:591</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea90091808850e51109fcb2f06fc8eb6f3"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea90091808850e51109fcb2f06fc8eb6f3">BEAGLE_FLAG_SCALERS_LOG</a></div><div class="ttdef"><b>Definition:</b> beagle.h:158</div></div>
<div class="ttc" id="struct_beagle_resource_html_adc4f25e6c9f6b62c0ca00d41fd5e99f7"><div class="ttname"><a href="struct_beagle_resource.html#adc4f25e6c9f6b62c0ca00d41fd5e99f7">BeagleResource::name</a></div><div class="ttdeci">char * name</div><div class="ttdef"><b>Definition:</b> beagle.h:212</div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfceaba333086a5777117202ed0f16109157a"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfceaba333086a5777117202ed0f16109157a">BEAGLE_ERROR_UNINITIALIZED_INSTANCE</a></div><div class="ttdef"><b>Definition:</b> beagle.h:125</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea40c7b4711118fb6fa14e697a698eda87"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea40c7b4711118fb6fa14e697a698eda87">BEAGLE_FLAG_FRAMEWORK_CUDA</a></div><div class="ttdef"><b>Definition:</b> beagle.h:177</div></div>
<div class="ttc" id="struct_beagle_operation_html"><div class="ttname"><a href="struct_beagle_operation.html">BeagleOperation</a></div><div class="ttdoc">A list of integer indices which specify a partial likelihoods operation. </div><div class="ttdef"><b>Definition:</b> beagle.h:589</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea9fc181aac842ebac6d51ccb19cf0e2ca"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea9fc181aac842ebac6d51ccb19cf0e2ca">BEAGLE_FLAG_INVEVEC_TRANSPOSED</a></div><div class="ttdef"><b>Definition:</b> beagle.h:161</div></div>
<div class="ttc" id="beagle_8h_html_ad0b1d6509865e06715cf96b7f5ec0b13"><div class="ttname"><a href="beagle_8h.html#ad0b1d6509865e06715cf96b7f5ec0b13">beagleResetScaleFactors</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleResetScaleFactors(int instance, int cumulativeScaleIndex)</div><div class="ttdoc">Reset scalefactors. </div></div>
<div class="ttc" id="beagle_8h_html_a9e61de870cc34893168a88fe6823dfce"><div class="ttname"><a href="beagle_8h.html#a9e61de870cc34893168a88fe6823dfce">BeagleReturnCodes</a></div><div class="ttdeci">BeagleReturnCodes</div><div class="ttdoc">Error return codes. </div><div class="ttdef"><b>Definition:</b> beagle.h:120</div></div>
<div class="ttc" id="beagle_8h_html_a3f3abf6b7c463b689a26ec83fb14bddea5a64736d6ca8cd54532e35f597671f16"><div class="ttname"><a href="beagle_8h.html#a3f3abf6b7c463b689a26ec83fb14bddea5a64736d6ca8cd54532e35f597671f16">BEAGLE_FLAG_EIGEN_COMPLEX</a></div><div class="ttdef"><b>Definition:</b> beagle.h:150</div></div>
<div class="ttc" id="beagle_8h_html_a72c7aac15b0cc06f03e6177ad0a161e6"><div class="ttname"><a href="beagle_8h.html#a72c7aac15b0cc06f03e6177ad0a161e6">beagleSetTransitionMatrices</a></div><div class="ttdeci">BEAGLE_DLLEXPORT int beagleSetTransitionMatrices(int instance, const int *matrixIndices, const double *inMatrices, const double *paddedValues, int count)</div><div class="ttdoc">Set multiple transition matrices. </div></div>
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